World Trade Center Disaster Identification Diary

Thursday, September 13  I managed to
collect my email while visiting London on the last leg of a several
week tour of Europe. Nancy and I had learned of the Trade Towers
attack from the television in our hotel in Haarlem where we were on
Tuesday. It was a bad end to a good
afternoon. Haarlem, a historically significant and easy-going
neighbor of Amsterdam (a reputedly easy-going place in its own right)
was the home of the riveting 17th century portraitist Frans Hals and
is today the home of the Frans Hals museum. So we  two people
with little understanding, appreciation, or interest in art 
had spent a fascinating hour or two perusing the collection of Hals
works that are accessible given the limited budget of a small museum.

Hals' Willem Coymans

Back at the hotel I had switched on the TV in time to see some of
the live action and numerous replays of now-familiar events,
accompanied by surprisingly little voice-over aside from a short
period during which a smug BBC commentator analyzed the context and
future significance of the goings-on until mercifully he was given
the hook.

My potential involvement

Wednesday morning we were slightly
affected by the attack in the sense that we waded through security
confusion when we flew out of Schiphol (Amsterdam) for London.
Moreover, in considering the talk that I was scheduled to present in
London, I hit on the idea to discuss the prospects for WTC
identifications.* But not until I read
my email message from Dr. Howard Baum of the Forensic Biology (i.e.
DNA) section of the Office of the Chief Medical Examiner of New York
did the possibility of my personal involvement with the disaster
occur to me. The OCME has been using the Kinship module of DNAVIEW for several years, and it is
already well established as a tool for
disaster body identification. I shouldn't have needed Howard to
remind me. His message was brief. He wrote, "We need help coping
with the mass disaster in New York City."

Howard's immediate thought was the application of the Kinship
program, but I thought I had even more to offer. There was going to be
a lot of genetic data to manipulate, whose exact nature couldn't be
predicted in advance. As one who has worked with computers since 1959,
earned a doctorate in mathematics, and done dozens of practical or
research projects involving DNA-relationship ideas and computations, I
figure I am uniquely prepared to perform whatever manipulations and
analysis might be necessary to wring information from the data.

Swissair identification paradigm

From earlier experience in disaster identification with the Swissair 111 crash, I assumed that there would be
a necessary "screening" step in making the WTC identifications based
on relatives; further, I could extrapolate that due to the larger
scale of the WTC problem new complexities would need to be faced
(links WTC prospectus and WTC Powerpoint above).

Screening  a rough but quick scan (<<1 second/comparison)
to select likely
candidate matches between victim and reference family samples by
comparing each individual reference with each victim sample
(millions of screening comparisons in the WTC case);

Testing  a candidate family-to-victim correspondence is
evaluated by using the Kinship program to
make the accurate computation (minutes/comparison) which considers the
family as a group (hopefully only a few thousand WTC relationships
will require testing and confirmation).

Benoit LeClair, then of the RCMP DNA group, had shown how the
screening could be done in that case with a mere Excel application,
based on sorting the DNA profiles such that similar profiles would be
sorted into neighboring positions. I considered his idea as a
starting point. But for the much larger dataset that the WTC
disaster might produce, I soon became convinced that more firepower
and algorithmic sophistication would be necessary.

The false-positive problem

The main difficulty that I foresaw emerging as the sizes of the
two lists  the victim list and the family reference list 
grow, is the increasing incidence of "false positives." If both lists
are small and some person C in the reference list has a brother who
died, and some profile V in the victim list looks like a brother of
C, it probably is. However, if the victim list has thousands of
profiles, then for any given reference person C there will be dozens
of victim profiles that coincidentally resemble C just as much as a
typical true brother does. The proportion of false positives
is proportional to the size of the victim list.

Therefore I was sure that a simple sorting program of the sort that
had been adequate for the Swissair identifications, would not be very
useful for the WTC disaster. Specifically, in my London talk on
September 13,
I hypothesized 

Of course the first several of my estimates have proven to be quite far off.
However, #4-8 are in the ballpark. The implication of the estimate #7 is, that for
every 1000 victims, there will be about one who coincidentally resembles any
given reference person to the same extent as does a true child. Thus, using
individual parents as references to fish victims out of the rubble would result
in more false leads than true ones. On the other hand, #5 implies that if a more
sophisticated trolling operation is used, wherein two reference parents are
simulataneously compared with each victim to accomplish a sort of
triangulation,
then the number of false hits will be very small. Point #9 is correct.

Work begins

Toward the end of September I outlined what I
felt I could contribute in a fax to Howard, and was gratified at his
prompt acceptance of my offer. He added a new task as well. Several
different computer programs had been offered to do the "screening" part of sorting out the
identifications; would I evaluate these offerings? Of course 
although admittedly my expectation was already that I would write my
own. As I later remarked to Howard's chief, Bob Shaler (head of the
Forensic Biology section), I thought I could write the program from
scratch faster than examine and evaluate the other possibilities. Bob
diplomatically accepted my remark, but of course held his ground.

The upshot was, on October 2, the first of
several trips to NY. Dr. Shaler organized a one-day meeting, a
"summit of genetics experts" (Wall Street Journal) to discuss various
problems and possible approaches for sorting through the inevitable
masses of data. Five laboratories  the city Office of the Chief
Medical Examiner, NY State Police, Bode Technologies, Myriad, and
Celera  who were expected to do parts of the DNA analysis were
represented. Coincidentally Myriad now included my old colleague
Benoit formerly of the RCMP. The FBI and myself were also present to
discuss software, as well as Howard Cash and others from a company
called GeneCodes that is contracted with the OCME to provide software.
Finally, there were a few people from the NIJ (National Institutes of
Justice, which is another arm of the DOJ). Following introductory
explanations by Bob Shaler in the morning several of us presented our
ideas about making the necessary victim-to-reference identifications.
The afternoon was mostly discussions, and of course mostly rather
general and oriented toward planning. From time to time, though,
people inevitably succumb to the temptation to discuss details even
when it is obvious that there is neither time nor yet sufficient
information to make a detailed discussion productive. When this
happened, Chief Inspector Dale of the State Police patiently
suggested, each time as if it were the first, that it would be
appropriate to make general plans. I enjoyed that.

At some juncture, concerned that the plans might be steering toward
an unnecessary and ponderous software project, I made a comment to the
same effect as I have indicated above, that once I am able to get my
hands on the data, I will quite quickly be able to produce the
tentative identifications by myself. At this Howard Cash piped in,
"Surely, Charles, even your work can stand a second opinion." I told
him he had a fair point.

WTC Kinship and Data Analysis Planning Panel (KADAP)

A few weeks later, on October 19-21, the
NIJ convened a distinguished panel of about 25 people of various
expertises in Albany, NY. The group included several people I knew
well from the forensic DNA community, and others, including a few I
had heard of, who I had the pleasure of meeting for the first time.

The three-day meeting ranged over a variety of topics. The one
topic originally mentioned to me was the same that Bob Shaler had
already asked of me: choose which screening program to use. To that
end I put together a Powerpoint presentation
to explain the difficulties and pitfalls as I foresaw  and, by
now, had computed.

In assessing the candidate screening programs, I had in mind
several design requirements:

"batch" operation

Most of the available programs stored a list of victim profiles,
and expected the user to perform, for each family to search against the
victim profile list, some manual operatons such as typing in the family
DNA profiles. That would be very awkward.

It implies spending at least several moments per family just for
screening, times a thousand or so families

and again each time there is an updated victim list.

It doesn't cater to "cherry picking"  concentrating first
on those families for which clear victim candidates pop up, rather
than wasting time on difficult or impossible cases.

likelihood ratio evaluation

The quick and dirty way to estimate if two profiles come from
related people is to count common alleles. This may be too dirty.

My simulations convinced me that more sophisticated (LR) computations, taking into
account for example that sharing rare alleles is more significant than
sharing common ones, would greatly improve the accuracy of the screening.

look for potential victim-family associations that
are indicated by at least two members of the same family
The already available programs scored poorly by the above criteria.
However, my preferred idea, to produce something from scratch, might
reasonably be considered deficient with respect to such standards as:

proven support; multiple support personel

validated performance

track record of reliability

Nonetheless, I naturally decided to go ahead with my own screening program.

Relatives identified

In any case, there was certainly no harm in trying. A lot of the most
difficult work for my intended screening module was embodied in
programs that I had already written in order run simulations to
decide what kind of screening program was likely to be effective, and
what kind of data likely to be sufficient. The first version of the
program took only a few days to write. Writing programs in a sterile
environment is easy. The acid test of a program is whether it works
with real data and  almost as important  real users. I
was anxious to get my hands on the lists of DNA profiles, which by
now were flowing out of Bode and Myriad labs and accumulating at the
NY State Police.

November 8, 2001  I went to the OCME
lab in NYC for a scheduled two-day visit to deliver Mark I of my new
software, collect some data, and try it out. Predictably, the
first look at the data showed some small surprises: the format of the
data was not exactly what I expected. I decided to stay around a few
extra days to sort everything out. Thus, I was in New York for the
astonishing incident of the following Monday.

November 10, 2001  The first
effective run of the screening program poured out a sorted list of
victim-family potential associations in about 5 minutes. The families
on the top of the list figured to be genuine identifications;
families with no strong resemblance to any victim sample would sort
further down. Indeed, the first victim-family pair on the list had an
extremely high score. Checking the actual profiles showed that this
case concerned identical twins, as I expected since I'd been
previously told that among the DNA identifications already made
through "direct" references was a person
who was the identical twin of a survivor.

Next on the list was another identical twin case. This
one  or at any rate at least one of the two  was a new
identification, the first I had found. The third candidate
identifications on the list was a case where the mother, the
daughter, and a brother had presented themselves as references.
The screening report only told me that two of these people bore
a resemblance to the same victim. To confirm the identity of that
victim, I needed to make a family-specific computation with the
Kinship program to check that the entire
assemblage is genetically consistent and numerically convincing.

It was. According to the kinship computation, it was either
the right victim, or it was a one-in-twenty-billion coincidence.
That's good enough to call it a confirmed identification.

And so it went, easily, for the first thirty or so cases, that
Saturday morning. Of the next twenty, some
looked ok but the data was often insufficient to be confident
according to the criteria we had established. A few looked to be
spurious. After that, the list started to run dry. The data simply
didn't exist to say who went with whom. More data was necessary,
both as to obtaining more reference family members, and recovering
further victims. Nor was I in a position to know which of the
identities I had found might already be known from direct DNA
references or from some other method.

American Airlines Flight 587

9am Monday, November 12, 2001  An
American Airlines flight crashed in Queens, almost within sight of
our hotel window. By the time I showed up at the OCME offices with my
list of relationship identifications, the WTC problem was temporarily
demoted in priority; plans were already being made to identify the
new tranche of victims. Obviously, this would be another test of my
new software.

We discussed the codings schemes that would be used for the
airplane victims, and I considered what minor modifications would be
needed. Plane crashes, unlike office environments, tend to include
related people. It's important to know about them and to consider
them in the analysis. Shaler and his colleagues were already thinking
about how to improve on the WTC experience in collecting samples from
relatives. It may seem a ghoulish observation, but an experienced
disaster identification team was swinging into action.

We left New York on Wednesday, figuring that
I had a bit of work to do.

Airplane crashes versus WTC attacks

Thursday, November 22, 2001  It
took only a few days to customize the program to accept the airline
crash data, and it also took the OCME only a week to begin producing
DNA typing data from the crash.

I believe that every disaster is unique. Contrary to the hope of a
few of the KADAP group, I don't believe it is practical or realistic
to expect a "disaster identification" program to be a result of the
current identification effort, or efforts. Useful tools, yes.
Worthwhile experience, also.

For example, a large part of the
difficulty of the WTC identifications is gathering, collating,
checking, and correcting data from a large variety of sources. There
is so much DNA typing to be done that it was of necessity farmed out
to several vendors, with inevitable consequent complications of
disparate sample coding schemes, and complexities in receiving the
data and in following up with questions about it. By contrast, the
airplane crash DNA analyses would all be done at the OCME lab.

Also, I have already mentioned the unique screening complexity
of the WTC disaster because of the sheer magnitude of combinations,
compared to those in a smaller disaster such as an airplane crash.

On the other hand, an airplane crash brings complexities of
its own: Typically there are numerous families who flew
and perished together. The fact that several different remains
are related to one another, and to the same sets of living references,
is both a difficulty and a hint that must be utilitized in
establishing identities (Kinship analysis when
there are many possibilities). The Trade Center victims include a
few relatives, and if we forgot to consider the possibility we would
surely announce some incorrect identifications, but they are the
exception.

In an airplane crash there is a reasonable chance to identify
every victim, and this "closed system" quality
of the problem, like a completed jig-saw puzzle, is helpful.

A war zone like Bosnia has other characteristics. For example, there
are many mass graves, but within each grave it is to be expected that the
victims originated from nearby. Therefore geographical and other non-DNA
or, as we have come to call it, "meta-data", plays
an important role.

In the case of AA587, the screening program sorted together the families
and victims rather easily as the data flowed in. There were a few family
groups, as point #3 above, that were tricky to unravel. In order to help
myself sort them out I added a new
feature to the Kinship program so that it instantly shows a helpful
diagram of all likely pair-wise relationship among a group of people.

Most of the AA587 victims were identified within a few weeks, which is
sensational. Announcement of the final identification took about three
months, as inevitably a few cases were delayed by special problems.

WTC Status

Status May 30, 2002

Trade Center excavation officially ended today with a ceremony at the
site. Since I was in the city and in six previous visits since
September 11 I never happened to visit ground zero, I decided to take
this last chance to have a look. It was a look a the back of a lot of
heads and some fences, and most excitingly of some neighboring
buildings that were draped with giant shrouds. Not much to see, but it
interested me.

No new victims will be found. It will take a few weeks for the DNA
profiles of the most recently excavated victim pieces to be reported.
Once those have been checked against the reference materials 
direct or indirect  already in hand, I expect a pause in
the identifications. Further progress will depend mainly on success
in the new DNA techologies that are being attempted, namely
SNP's and
mtDNA.

For some victims blood samples were available, e.g. from blood donors.

Clothing, towels were rarely productive.

80% of the victims were men.

Status June 24, 2003

The 1000th victim identification was announced on April 29, 2002, seven
months after the attack. The 1500th identification came out on June 18, 2003, after 21 months.
The rate now seems to be two or three per week.
It is to be expected that progress has slowed, but not much can be
extrapolated. Identifications from traditional forensic STR loci and
primers ground pretty much to a halt several months ago. Special,
shorter versions of them  credit to John Butler and Bode
Technologies  then revived progress as I understand from Bob
Shaler, and similarly assistance from the other new technologies may
have either incremental or dramatic benefits.

Last July Bruce Weir suggested that I submit
an article on World Trade
identifications to an edition of Theoretical Population Genetics 
as the name implies a rather high-brow scientific journal  that he
was editing. He thought "it would have high interest," and so it proved.
The article, completed with Bruce's considerable help and co-authorship,
attracted what is by my standards a lot of interest. I gave an interview
to a German radio (in English) and a newspaper, to the children's science
magazine Odyssey, and to
Nature.com.

One point I made in the article was an estimate of the maximum
number of bodies for which any DNA has been found. I did this
probabalistically, trying to account for those victim fragments that
produced any DNA at all. If we then make the optimistic assumption
that all such fragments can eventually, through ultimately
sophisticated DNA typing methods, be identified, as many as 2100
victims might eventually be identified. Perhaps a better way to put
it is that no more than 2100 will be found. Dr. Hirsch, the NY Chief
Medical Examiner, has expressed his commitment to continue with the
work possibly for a long time, with a goal in mind of 2000
identifications. I agree that even that number seems very difficult.

SNP progress

Identification through SNP's seems promising. The theory is that SNP's
may succeed where STR's fail because the necessary extant DNA fragment
size is smaller. Successful STR typing depends on finding intact some
particular 120 to 300 (depending on the locus and the allele) base
pair stretch of DNA. Of this stretch, perhaps 20 to 120 bases is the
variable part that represents information (the information is in fact
the length of the variable part) and the remainder, the flanking
region, is partly a handle or label that selects the fragment of
interest uniquely from the entire genome, and partly a spacer included
in order to enable multiplexing  the assay of multiple loci in
the same test tube.

Orchid Biosciences has developed a high-speed, high-throughput,
largely automated method for SNP typing, which is being used for WTC
samples.

For SNP's, the region of interest is a single nucleotide, which
considerably reduces the fragment size. Moreover, the method by which
multiple assays are acheived is entirely different, so there is no
need for a spacer in the flanking region. Consequently SNP's may
succeed where STR's fail when the DNA has degraded to the point where
the typical fragment size is around 100 bp.

Over 5000 samples, some victims, some from living relatives,
have been typed. The attempted panel of typing is 70 loci. Given that
many of the samples are degraded, as we already know from the mixed
success of STR typing, there is mixed success in SNP typing. Often
only a partial profile is obtained. However, for sure there are times
that SNP is quite successful even though STR was not. For these
cases the SNP technology is quite likely to provide new identifications.
Additionally, there will be cases where both technologies are only
moderately successful but the combination is just good enough.

mtDNA progress

*In subsequent months of course my (my)
idea, to link anything and everything to the Trade Tower attack, has
been widely copied. At the time, it seemed quite bright and original.